Flaviviridae are a group of positive, single-stranded RNA viruses with a genome size from 9 to 15 kb. They are enveloped viruses of approximately 40 to 50 nm. An overview of the Flaviviridae taxonomy is available from the International Committee for Taxonomy of Viruses. The group Flaviviridae consists of three genera.                1. Flaviviruses. This genus includes the Dengue virus group (Dengue virus, Dengue virus type 1, Dengue virus type 2, Dengue virus type 3, Dengue virus type 4), the Japanese encephalitis virus group (Alfuy Virus, Japanese encephalitis virus, Kookaburra virus, Koutango virus, Kunjin virus, Murray Valley encephalitis virus, St. Louis encephalitis virus, Stratford virus, Usutu virus, West Nile virus), the Modoc virus group, the Rio Bravo virus group (Apoi virus, Rio Bravo virus, Saboya virus), the Ntaya virus group, the Tick-Borne encephalitis group (tick-born encephalitis virus), the Tyuleniy virus group, Uganda S virus group, and the Yellow Fever virus group. Apart from these major groups, there are some additional Flaviviruses that are unclassified.        2. Hepaciviruses. This genus contains only one species, the hepatitis C virus (HCV), which is composed of many clades, types and subtypes.        3. Pestiviruses. This genus includes bovine viral diarrhea virus-2 (BVDV-2), Pestivirus type 1 (including BVDV), pestivirus type 2 (including hog cholera virus), and pestivirus type 3 (including border disease virus).        
One of the most important Flaviviridae infections in humans is caused by the hepatitis C virus (HCV). This is the second major cause of viral hepatitis, with an estimated 170 million carriers world-wide (World Health Organization; Hepatitis C: global prevalence, Weekly Epidemiological Record, 1997, 72, 341), 3.9 million of whom reside in the United States (Centers for Disease Control; unpublished data, http://www.cdc.gov/ncidod/diseases/hepatitis/heptab3.htm).
The genomic organization of the Flaviviridae share many common features. The HCV genome is often used as a model. HCV is a small, enveloped virus with a positive, single-stranded RNA genome of −9.6 kb within the nucleocapsid. The genome contains a single open reading frame (ORF) encoding a polyprotein of just over 3,000 amino acids, which is cleaved to generate the mature structural and nonstructural viral proteins. The ORF is flanked by 5′ and 3′ non-translated regions (NTRs) of a few hundred nucleotides in length, which are important for RNA translation and replication. The translated polyprotein contains the structural core (C) and envelope proteins (E1, E2, p7) at the N-terminus, followed by the nonstructural proteins (NS2, NS3, NS4A, NS4B, NS5A, NS5B). The mature structural proteins are generated via cleavage by the host signal peptidase (see Hijikata, M. et al., Proc. Nat. Acad. Sci., USA, 1991, 88, 5547; Hussy, P. et al., Virology, 1996, 224, 93; Lin, C. et al., J. Virol., 1994, 68, 5063; Mizushima, H. et al., J. Virol., 1994, 68, 2731; Mizushima, H. et al., J. Virol., 1994, 68, 6215; Santolini, E. et al., J. Virol., 1994, 68, 3631; Selby, M. J. et al., Virology, 1994, 204, 114; and Grakoui, A. et al., Proc. Nat. Acad. Sci., USA, 1993, 90, 10538). The junction between NS2 and NS3 is autocatalytically cleaved by the NS2/NS3 protease (see Hijikata, M. et al., J. Virol., 1993, 67, 4665 and Bartenschlager, R. et al., J. Virol., 1994, 68, 5045), while the remaining four junctions are cleaved by the N-terminal serine protease domain of NS3 complexed with NS4A (see Fulla, C. et al., J. Virol., 1994, 68, 3753; Lin, C. et al., J. Virol., 1994, 68, 8147; Tanji, Y. et al., J. Virol., 1995, 69, 1575; and Tai, C. L. et al., J. Virol., 1996, 70, 8477). The NS3 protein also contains the nucleoside triphosphate (NTP)-dependent helicase activity which unwinds duplex RNA during replication. The NS5B protein possesses RNA-dependent RNA polymerase (RDRP) activity (see Behrens, S. E. et al., EMBO J., 1996, 15, 12; Lohmann, V. et al., J. Virol., 1997, 71, 8416-8428; and Lohmann, V. et al., Virology, 1998, 249, 108), which is essential for viral replication, (Ferrari, E. et al., J. Virol., 1999, 73, 1649). Unlike HBV or HIV, no DNA is involved in the replication of HCV.
Treatment of HCV Infection with Ribavirin
Ribavirin (1-β-D-ribofuranosyl-1H-1,2,4-triazole-3-carboxamide) is a synthetic, non-interferon-inducing, broad-spectrum antiviral nucleoside analog sold under the trade name VIRAZOLE® (Merck Index, 11th edition, Editor: Budavari, S., Merck & Co., Inc., Rahway, N.J., p. 1304, 1989). U.S. Pat. Nos. 3,798,209 and RE 29,835 disclose and claim ribavirin. Ribavirin is structurally similar to guanosine, and has in vitro activity against several DNA and RNA viruses including Flaviviridae (Gary L. Davis, Gastroenterology 118:S104-S114, 2000).
Ribavirin reduces serum amino transferase levels to normal in 40% of patients, but it does not lower serum levels of HCV-RNA (Gary L. Davis, Gastroenterology 118:S104-S114, 2000). Thus, ribavirin alone is not effective in reducing viral RNA levels. Additionally, ribavirin has significant toxicity and is known to induce anemia.
Ribavirin is not approved for monotherapy against HCV. It has been approved in combination with interferon alpha-2a or interferon alpha-2b for the treatment of HCV.
Treatment of HCV Infection with Interferon
Interferons (IFNs) have been commercially available for the treatment of chronic hepatitis for nearly a decade. IFNs are glycoproteins produced by immune cells in response to viral infection. IFNs inhibit replication of a number of viruses, including HCV, and when used as the sole treatment for hepatitis C infection, IFN can in certain cases suppress serum HCV-RNA to undetectable levels. Additionally, IFN can normalize serum amino transferase levels. Unfortunately, the effect of IFN is temporary, and a sustained response occurs in only 8%-9% of patients chronically infected with HCV (Gary L. Davis, Gastroenterology 118:S104-S114, 2000). Most patients, however, have difficulty tolerating interferon treatment, which causes severe flu-like symptoms, weight loss, and lack of energy and stamina.
A number of patents disclose Flaviviridae, including HCV, treatments, using interferon-based therapies. For example, U.S. Pat. No. 5,980,884 to Blatt et al. discloses methods for retreatment of patients afflicted with HCV using consensus interferon. U.S. Pat. No. 5,942,223 to Bazer et al. discloses an anti-HCV therapy using ovine or bovine interferon-tau. U.S. Pat. No. 5,928,636 to Alber et al. discloses the combination therapy of interleukin-12 and interferon alpha for the treatment of infectious diseases including HCV. U.S. Pat. No. 5,849,696 to Chretien et al. discloses the use of thymosins, alone or in combination with interferon, for treating HCV. U.S. Pat. No. 5,830,455 to Valtuena et al. discloses a combination HCV therapy employing interferon and a free radical scavenger. U.S. Pat. No. 5,738,845 to Imakawa discloses the use of human interferon tau proteins for treating HCV. Other interferon-based treatments for HCV are disclosed in U.S. Pat. No. 5,676,942 to Testa et al., U.S. Pat. No. 5,372,808 to Blatt et al., and U.S. Pat. No. 5,849,696. A number of patents also disclose pegylated forms of interferon, such as, U.S. Pat. Nos. 5,747,646, 5,792,834, and 5,834,594 to Hoffmann-La Roche Inc; PCT Publication Nos. WO 99/32139 and WO 99/32140 to Enzon; WO 95/13090 and U.S. Pat. Nos. 5,738,846 and 5,711,944 to Schering; and U.S. Pat. No. 5,908,621 to Glue et al.
Interferon alpha-2a and interferon alpha-2b are currently approved as monotherapy for the treatment of HCV. ROFERON®-A (Roche) is the recombinant form of interferon alpha-2a. PEGASYS® (Roche) is the pegylated (i.e. polyethylene glycol modified) form of interferon alpha-2a. INTRON®A (Schering Corporation) is the recombinant form of interferon alpha-2b, and PEG-INTRON® (Schering Corporation) is the pegylated form of interferon alpha-2b.
Other forms of interferon alpha, as well as interferon beta, gamma, tau, and omega are currently in clinical development for the treatment of HCV. For example, INFERGEN® (interferon alphacon-1) by InterMune, OMNIFERON® (natural interferon) by Viragen, ALBUFERON® by Human Genome Sciences, REBIF® (interferon beta-1a) by Ares-Serono, omega interferon by BioMedicine, oral interferon alpha by Amarillo Biosciences, and interferon gamma, interferon tau, and interferon gamma-1b by InterMune are in development.
Combination of Interferon and Ribavirin
The current standard of care for chronic hepatitis C is combination therapy with an alpha interferon and ribavirin. The combination of interferon and ribavirin for the treatment of HCV infection has been reported to be effective in the treatment of interferon naïve patients (Battaglia, A. M. et al., Ann. Pharmacother. 34:487-494, 2000), as well as for treatment of patients when histological disease is present (Berenguer, M. et al., Antivir. Ther. 3(Suppl. 3):125-136, 1998). Studies have shown that more patients with hepatitis C respond to pegylated interferon-alpha/ribavirin combination therapy than to combination therapy with unpegylated interferon alpha. However, as with monotherapy, significant side effects develop during combination therapy, including hemolysis, flu-like symptoms, anemia, and fatigue. (Gary L. Davis, Gastroenterology 118:S104-S114, 2000).
Combination therapy with PEG-INTRON® (peginterferon alpha-2b) and REBETOL® (ribavirin, USP) Capsules is available from Schering Corporation. REBETOL® (Schering Corporation) has also been approved in combination with INTRON® A (interferon alpha-2b, recombinant, Schering Corporation). Roche's PEGASYS® (pegylated interferon alpha-2a) and COPEGUS® (ribavirin) are also approved for the treatment of HCV.
PCT Publication Nos. WO 99/59621, WO 00/37110, WO 01/81359, WO 02/32414, and WO 03/024461 by Schering Corporation disclose the use of pegylated interferon alpha and ribavirin combination therapy for the treatment of HCV. PCT Publication Nos. WO 99/15194, WO 99/64016, and WO 00/24355 by Hoffmann-La Roche Inc also disclose the use of pegylated interferon alpha and ribavirin combination therapy for the treatment of HCV.
Additional References Disclosing Methods to Treat HCV Infections
A number of HCV treatments are reviewed by Dymock et al. in Antiviral Chemistry & Chemotherapy, 11:2; 79-96 (2000).
Several substrate-based NS3 protease inhibitors have been identified in the literature, in which the scissile amide bond of a cleaved substrate is replaced by an electrophile, which interacts with the catalytic serine. Attwood et al. (1998), Antiviral peptide derivatives, WO 98/22496; Attwood et al. (1999), Antiviral Chemistry and Chemotherapy 10:259-273; Attwood et al. (1999), Preparation and use of amino acid derivatives as antiviral agents, German Patent Publication DE 19914474; Tung et al. (1998), Inhibitors of serine proteases, particularly hepatitis C virus NS3 protease, WO 98/17679. The reported inhibitors terminate in an electrophile such as a boronic acid or phosphonate. Llinas-Brunet et al. (1999), Hepatitis C inhibitor peptide analogues, WO 99/07734. Two classes of electrophile-based inhibitors have been described, alphaketoamides and hydrazinoureas.
The literature has also described a number of non-substrate-based inhibitors. For example, evaluation of the inhibitory effects of 2,4,6-trihydroxy-3-nitro-benzamide derivatives against HCV protease and other serine proteases has been reported. Sudo, K. et al., (1997) Biochemical and Biophysical Research Communications, 238:643-647; Sudo, K. et al., (1998) Antiviral Chemistry and Chemotherapy 9:186. Using a reverse-phase HPLC assay, the two most potent compounds identified were RD3-4082 and RD3-4078, the former substituted on the amide with a 14-carbon chain and the latter possessing a para-phenoxyphenyl group.
Thiazolidine derivatives have been identified as micromolar inhibitors, using a reverse-phase HPLC assay with an NS3/4A fusion protein and NS5A/5B substrate. Sudo, K. et al., (1996) Antiviral Research 32:9-18. Compound RD-1-6250, possessing a fused cinnamoyl moiety substituted with a long alkyl chain, was the most potent against the isolated enzyme. Two other active examples were RD4 6205 and RD4 6193.
Other literature reports screening of a relatively small library using an ELISA assay and the identification of three compounds as potent inhibitors, a thiazolidine and two benzanilides. Kakiuchi N. et al., J. EBS Letters 421:217-220; Takeshita N. et al., Analytical Biochemistry 247:242-246, 1997. Several U.S. patents disclose protease inhibitors for the treatment of HCV. For example, U.S. Pat. No. 6,004,933 to Spruce et al. discloses a class of cysteine protease inhibitors for inhibiting HCV endopeptidase 2. U.S. Pat. No. 5,990,276 to Zhang et al. discloses synthetic inhibitors of hepatitis C virus NS3 protease. The inhibitor is a subsequence of a substrate of the NS3 protease or a substrate of the NS4A cofactor. The use of restriction enzymes to treat HCV is disclosed in U.S. Pat. No. 5,538,865 to Reyes et al.
Isolated from the fermentation culture broth of Streptomyces sp., Sch 68631, a phenanthrenequinone, possessed micromolar activity against HCV protease in a SDS-PAGE and autoradiography assay. Chu M. et al., Tetrahedron Letters 37:7229-7232, 1996. In another example by the same authors, Sch 351633, isolated from the fungus Penicillium griseofulvum, demonstrated micromolar activity in a scintillation proximity assay. Chu M. et al., Bioorganic and Medicinal Chemistry Letters 9:1949-1952, 1999. Nanomolar potency against the HCV NS3 protease enzyme has been achieved by the design of selective inhibitors based on the macromolecule eglin c. Eglin c, isolated from the leech, is a potent inhibitor of several serine proteases such as S. griseus proteases A and B, α-chymotrypsin, chymase, and subtilisin. Qasim M. A. et al., Biochemistry 36:1598-1607, 1997.
HCV helicase inhibitors have also been reported. U.S. Pat. No. 5,633,358 to Diana G. D. et al.; PCT Publication No. WO 97/36554 to Diana G. D. et al. There are a few reports of HCV polymerase inhibitors: some nucleotide analogues, gliotoxin, and the natural product cerulenin. Ferrari R. et al., Journal of Virology 73:1649-1654, 1999; Lohmann V. et al., Virology 249:108-118, 1998.
Antisense phosphorothioate oligodeoxynucleotides complementary to sequence stretches in the 5′-non-coding region of the HCV are reported as efficient inhibitors of HCV gene expression in in vitro translation and HepG2 HCV-luciferase cell culture systems. Alt M. et al., Hepatology 22:707-717, 1995. Recent work has demonstrated that nucleotides 326-348 comprising the 3′-end of the NCR and nucleotides 371-388 located in the core coding region of the HCV RNA are effective targets for antisense-mediated inhibition of viral translation. Alt M. et al., Archives of Virology 142:589-599, 1997. U.S. Pat. No. 6,001,990 to Wands et al. discloses oligonucleotides for inhibiting the replication of HCV. PCT Publication No. WO 99/29350 discloses compositions and methods of treatment for hepatitis C infection comprising the administration of antisense oligonucleotides that are complementary and hybridizable to HCV RNA. U.S. Pat. No. 5,922,857 to Han et al. disclose nucleic acids corresponding to the sequence of the pestivirus homology box IV area for controlling the translation of HCV. Antisense oligonucleotides as therapeutic agents have been recently reviewed (Galderisi U. et al., Journal of Cellular Physiology 181:251-257, 1999).
Other compounds have been reported as inhibitors of IRES-dependent translation in HCV. Japanese Patent Publication JP-08268890 of Ikeda, N. et al.; Japanese Patent Publication JP-10101591 of Kai, Y. et al. Nuclease-resistant ribozymes have been targeted at the IRES and recently reported as inhibitors in an HCV-poliovirus chimera plaque assay. Maccjak D. J. et al., Hepatology 30 abstract 995, 1999. The use of ribozymes to treat HCV is also disclosed in U.S. Pat. No. 6,043,077 to Barber et al. and U.S. Pat. Nos. 5,869,253 and 5,610,054 to Draper et al.
Other patents disclose the use of immune system potentiating compounds for the treatment of HCV. For example, U.S. Pat. No. 6,001,799 to Chretien et al. discloses a method of treating HCV in non-responders to interferon treatment by administering an immune system-potentiating dose of thymosin or a thymosin fragment. U.S. Pat. Nos. 5,972,347 to Eder et al. and 5,969,109 to Bona et al. disclose antibody-based treatments for HCV infection.
U.S. Pat. No. 6,034,134 to Gold et al. discloses certain NMDA receptor agonists having immunomodulatory, antimalarial, anti-Borna virus, and anti-HCV activities. The disclosed NMDA receptor agonists belong to a family of 1-amino-alkylcyclohexanes. U.S. Pat. No. 6,030,960 to Morris-Natschke et al. discloses the use of certain alkyl lipids to inhibit the production of hepatitis-induced antigens, including those produced by HCV. U.S. Pat. No. 5,922,757 to Chojkier et al. discloses the use of vitamin E and other antioxidants to treat hepatic disorders including HCV. U.S. Pat. No. 5,858,389 to Elsherbi et al. discloses the use of squalene for treating HCV infection. U.S. Pat. No. 5,849,800 to Smith et al. discloses the use of amantadine for treatment of HCV infection. U.S. Pat. No. 5,846,964 to Ozeki et al. discloses the use of bile acids for treating HCV infection. U.S. Pat. No. 5,491,135 to Blough et al. discloses the use of N-(phosphonoacetyl)-L-aspartic acid to treat flavivirus infections, such as HCV infection.
Other compounds proposed for treating HCV infection include plant extracts (U.S. Pat. No. 5,837,257 to Tsai et al., U.S. Pat. No. 5,725,859 to Omer et al., and U.S. Pat. No. 6,056,961), piperidenes (U.S. Pat. No. 5,830,905 to Diana et al.), benzenedicarboxamides (U.S. Pat. No. 5,633,388 to Diana et al.), polyadenylic acid derivatives (U.S. Pat. No. 5,496,546 to Wang et al.), 2′,3′-dideoxyinosine (U.S. Pat. No. 5,026,687 to Yarchoan et al.), and benzimidazoles (U.S. Pat. No. 5,891,874 to Colacino et al.).
Other agents for the treatment of HCV infection include PEGASYS® (pegylated interferon alfa-2a) by Roche, INFERGEN® (interferon alfacon-1) by InterMune, OMNIFERON® (natural interferon) by Viragen, ALBUFERON® (albinterferon alpha 2b) by Human Genome Sciences, REBIF® (interferon beta-1a) by Ares-Serono, omega interferon by BioMedicine, oral interferon alpha by Amarillo Biosciences, interferon gamma-1b by InterMune, interleukin-10 by Schering-Plough, IP-501 by Interneuron, merimebodib VX-497 by Vertex, SYMMETREL® (amantadine) by Endo Labs Solvay, HEPTAZYME® by RPI, IDN-6556 by Idun Pharma., XTL-002 by XTL, HCV/MF59 by Chiron, CIVACIR® (hepatitis C immune globulin) by NABI, levovirin by ICN, viramidine by ICN, ZADAXIN® (thymosin alfa-1) by Sci Clone, CEPLENE® (histamine dihydrochloride) by Maxim, telaprevir VX 950/LY 570310 by Vertex/Eli Lilly, ISIS 14803 by Isis Pharmaceutical/Elan, IDN-6556 by Idun Pharmaceuticals, Inc., and JTK 003 by AKROS Pharma.
BioChem Pharma Inc. disclosed the use of various 1,3-dioxolane nucleosides for the treatment of a Flaviviridae infection in International Publication No. WO 01/32153.
BioChem Pharma Inc. also disclosed various other 2′-halo, 2′-hydroxy, and 2′-alkoxy nucleosides for the treatment of a Flaviviridae infection in International Publication No. WO 01/60315.
Idenix Pharmaceuticals, Ltd. discloses branched nucleosides and their use in the treatment of HCV and flaviviruses and pestiviruses in International Publication Nos. WO 01/90121 and WO 01/92282, respectively and U.S. Publication Nos. 2003/0050229 A1 and 2003/0060400 A1. A method for the treatment of HCV and flavivirus and pestivirus infections in humans and other host animals is disclosed that includes administering an effective amount of a biologically active 1′, 2′, and 3′-branched β-D or β-L nucleosides or a pharmaceutically acceptable salt or prodrug thereof, administered either alone or in combination, optionally in a pharmaceutically acceptable carrier.
International Publication Nos. WO 02/18404 and WO 02/100415 to F. Hoffmann-La Roche AG disclose various nucleoside analogs for the treatment of HCV RNA replication.
Pharmasset Limited, in WO 02/32920, discloses various nucleosides for the treatment of a variety of viruses, including Flaviviridae, and in particular HCV.
Merck & Co., Inc. and Isis Pharmaceuticals disclose in International Publication Nos. WO 02/057287 and WO 02/057425 and U.S. Publication No. 2002/0147160 A1 various nucleosides, and in particular several pyrrolopyrimidine nucleosides, for the treatment of viruses whose replication is dependent upon RNA-dependent RNA polymerase, including Flaviviridae, and in particular HCV.
In view of the severity of diseases associated with pestiviruses and flaviviruses, and their pervasiveness in animals, including humans, it is an object of the present invention to provide a compound, method, and composition for the treatment of a host, including animals and especially humans, infected with flavivirus or pestivirus.
It is a further object to provide a compound, method, and composition for the treatment of a host, including animals and especially humans, infected with hepaciviruses.